External Email - Use Caution
Dear Freesurfer Experts, I have two questions that I hope are easy to answer.
1. Would the calculation for E-TIV change if I edited the pial and reran recon-all as in this tutorial below? https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits_freeview
My understanding is that E-TIV should not change after minor edits to the pial segmentation, because the transform happens before these edits even happen. We start the at autorecon2-pial for the pial correction, which is after the Talairach transform computation.
2. I have two different windows computers with two VMware workstations running what I thought were the same versions of CentOS. They are both CentOS 6, but one is 6.5 and the other is 6.9. If both VMware workstations run the exact same versions of Freesurfer 6 (freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c), is it a problem if the CentOS versions are slightly different?
I know the FS wiki says "it is essential to process all your subjects with the same version of FreeSurfer, on the same OS platform and vendor, and for safety, even the same version of the OS.", but would there be enough of a difference between CentOS 6.5 and 6.9 to cause major discrepancies in Freesurfer T1 processing?
Thanks so much, Jeff
Hi Jeff
1. This should be fine.
2. I would think this is ok as well, but maybe you should run a few subjects on both and see if there are significant differences cheers Bruce On Thu, 7 Jun 2018, Jeff Crawford wrote:
External Email - Use Caution
Dear Freesurfer Experts,
I have two questions that I hope are easy to answer.
1. Would the calculation for E-TIV change if I edited the pial and reran recon-all as in this tutorial below?
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits_freeview
My understanding is that E-TIV should not change after minor edits to the pial segmentation, because the transform happens before these edits even happen. We start the at autorecon2-pial for the pial correction, which is after the Talairach transform computation.
2. I have two different windows computers with two VMware workstations running what I thought were the same versions of CentOS. They are both CentOS 6, but one is 6.5 and the other is 6.9. If both VMware workstations run the exact same versions of Freesurfer 6 (freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c), is it a problem if the CentOS versions are slightly different?
I know the FS wiki says “it is essential to process all your subjects with the same version of FreeSurfer, on the same OS platform and vendor, and for safety, even the same version of the OS.”, but would there be enough of a difference between CentOS 6.5 and 6.9 to cause major discrepancies in Freesurfer T1 processing?
Thanks so much,
Jeff
External Email - Use Caution
Thanks so much for the reply, Bruce.
I just had a follow up to question to #1. If E-TIV is calculated early on is the process, what is the minimum amount of recon I would need to run to be able to calculate that value? Say I was only interested in Freesurfer's E-TIV and not the cortical parcellation and subcortical segmentation.
My guess is that I would run "autorecon1" to run the "talairach transform computation" , which would produce the talairach.xfm. Then run mri_segstats with an "etiv" flag to "Compute intercranial volume from subject/mri/transforms/talairach.xfm" like in this explanation: https://surfer.nmr.mgh.harvard.edu/fswiki/mri_segstats
Does this make sense?
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Bruce Fischl Sent: Thursday, June 07, 2018 10:15 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] E-TIV and Linux version: Some quick questions
Hi Jeff
1. This should be fine.
2. I would think this is ok as well, but maybe you should run a few subjects on both and see if there are significant differences cheers Bruce On Thu, 7 Jun 2018, Jeff Crawford wrote:
External Email - Use Caution
Dear Freesurfer Experts,
I have two questions that I hope are easy to answer.
1. Would the calculation for E-TIV change if I edited the pial and reran recon-all as in this tutorial below?
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits_freevie w
My understanding is that E-TIV should not change after minor edits to the pial segmentation, because the transform happens before these edits even happen. We start the at autorecon2-pial for the pial correction, which is after the Talairach transform computation.
2. I have two different windows computers with two VMware workstations running what I thought were the same versions of CentOS. They are both CentOS 6, but one is 6.5 and the other is 6.9. If both VMware workstations run the exact same versions of Freesurfer 6 (freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c), is it a problem if the CentOS versions are slightly different?
I know the FS wiki says “it is essential to process all your subjects with the same version of FreeSurfer, on the same OS platform and vendor, and for safety, even the same version of the OS.”, but would there be enough of a difference between CentOS 6.5 and 6.9 to cause major discrepancies in Freesurfer T1 processing?
Thanks so much,
Jeff
yes, I think that is correct On Thu, 7 Jun 2018, Jeff Crawford wrote:
External Email - Use CautionThanks so much for the reply, Bruce.
I just had a follow up to question to #1. If E-TIV is calculated early on is the process, what is the minimum amount of recon I would need to run to be able to calculate that value? Say I was only interested in Freesurfer's E-TIV and not the cortical parcellation and subcortical segmentation.
My guess is that I would run "autorecon1" to run the "talairach transform computation" , which would produce the talairach.xfm. Then run mri_segstats with an "etiv" flag to "Compute intercranial volume from subject/mri/transforms/talairach.xfm" like in this explanation: https://surfer.nmr.mgh.harvard.edu/fswiki/mri_segstats
Does this make sense?
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Bruce Fischl Sent: Thursday, June 07, 2018 10:15 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] E-TIV and Linux version: Some quick questions
Hi Jeff
This should be fine.
I would think this is ok as well, but maybe you should run a few subjects on both and see if there are significant differences cheers Bruce On Thu, 7 Jun 2018, Jeff Crawford wrote:
External Email - Use Caution
Dear Freesurfer Experts,
I have two questions that I hope are easy to answer.
1. Would the calculation for E-TIV change if I edited the pial and reran recon-all as in this tutorial below?
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits_freevie w
My understanding is that E-TIV should not change after minor edits to the pial segmentation, because the transform happens before these edits even happen. We start the at autorecon2-pial for the pial correction, which is after the Talairach transform computation.
2. I have two different windows computers with two VMware workstations running what I thought were the same versions of CentOS. They are both CentOS 6, but one is 6.5 and the other is 6.9. If both VMware workstations run the exact same versions of Freesurfer 6 (freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c), is it a problem if the CentOS versions are slightly different?
I know the FS wiki says “it is essential to process all your subjects with the same version of FreeSurfer, on the same OS platform and vendor, and for safety, even the same version of the OS.”, but would there be enough of a difference between CentOS 6.5 and 6.9 to cause major discrepancies in Freesurfer T1 processing?
Thanks so much,
Jeff
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